Download MendeleyCrystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
1VK6
Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution
- PDB DOI: https://doi.org/10.2210/pdb1VK6/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli K-12
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2004-04-30 Released: 2004-05-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.220
- R-Value Work: 0.187
- R-Value Observed: 0.188
wwPDB Validation 3D Report Full Report
This is version 1.4 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NADH pyrophosphatase | A | 269 | Escherichia coli K-12 | Mutation(s): 8 Gene Names: nudC, b3996, yjaD, JW5548 EC: 3.6.1 (PDB Primary Data), 3.6.1.22 (UniProt) |  |
UniProt | |||||
Find proteins for P32664 (Escherichia coli (strain K12)) Explore P32664 Go to UniProtKB: P32664 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P32664 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | C [auth A], D [auth A], E [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | Ligand Interaction | |
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.220
- R-Value Work: 0.187
- R-Value Observed: 0.188
- Space Group: P 65 2 2
- Diffraction Data: https://doi.org/10.18430/M31VK6
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 127.319 | α = 90 |
| b = 127.319 | β = 90 |
| c = 108.405 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| SCALA | data scaling |
| CNS | refinement |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2004-05-11 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2004-05-11
Type: Initial release - Version 1.1: 2008-04-26
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
